I recently purchased two SEs, one 64GB model just as they were purging stock in preparation for the 128GB release, then I purchased one of the 128GB because they were being heavily discounted. Just my luck that the 128GB unit is the one with the inferior screen.
The 128GB unit's screen is inferior in multiple ways.
Firstly, it has the issue described in this thread. There is flicker with the supplied slide at higher brightness level, a weird flicker that messes with your brain because it's right on the edge of perception when looking square at the screen, but becomes more noticeable when you're moving your eyes. This is the kind of flicker that I can imagine some people being more sensitive to than others, and maybe some people can't see it even if their phone is doing it. I haven't seen any pseudo scan lines or flicker in normal images (yet), so I would probably not have been too worried about this one issue in isolation. The 64GB unit has zero flicker on that slide, regardless of brightness.
The 128GB unit's screen is also noticeably warmer, and it's blacks aren't as deep. The backlight brightness is the same, but the 64GB unit has less "glow". The distinctly different black screen characteristics make me suspect that, in addition to the A9 lottery, the iPhone SE might also be subject to a LCD panel lottery.
For the record, the serial numbers on both units start with DX3.